title: Aurora-A tumor10

status: Public on May 27 2010

type: genomic

city: Aurora

first: Enrique

last: Torchia

state: CO

department: Dermatology

country: USA

institute: University of Denver

description: Experimental group

hyb_protocol: labelled samples were prepared for hybridization using the Agilent aCGH Hybridization Kit and hybridized to arrays using Agilent Hybridization Oven (G2545A).

scan_protocol: Washed and dryed slides were scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: The Agilent Feature Extraction Software (v 9.5.31) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Mus musculus

source_name: Squamous Cell Carcinoma

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 5.0  was followed to label 1 µg of experimental or reference DNA

extract_protocol: Genomic DNA extracted using Dneasy Kit following manufacturer's instructions

tag: tumor type

value: SCC

tag: tissue

value: Skin

source_name: C57BL/6 reference genomic DNA

tag: strain


title: Burn wound margin pool >7 days post-thermal injury-1

status: Public on May 23 2010

type: RNA

city: Nashville

first: Lillian

middle: B

last: Nanney

state: TN

department: Plastic Surgery

institute: Vanderbilt University

description: All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.

hyb_protocol: Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

data_processing: For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Burn wound margin of human skin, replicate #1 of pooled time group >7 days post-thermal injury

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).  Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

extract_protocol: At the time of isolation, tissues were chopped into small pieces at -20°C.  Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample.  RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification.  RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate).  DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set.  Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample.  Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts.  RNA was re-suspended in RNase/DNase free H2O.  A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis.  If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.

tag: median age

tag: mean age

tag: Procedure

value: excision, right abdomen; excision, back; excision, chest; excision, right lower extremity; excision, right upper extremity

tag: Total Body Surface Are Burned

tag: Post Burn Day

tag: Sex

value: M; M; M; M; F


title: Aurora-A tumor11

description: Experimental group


title: Aurora-A tumor5

description: Experimental group


title: Aurora-A tumor7

description: Experimental group


title: Normal human (no thermal injury) skin pool control-3

source_name: Normal human skin, pooled replicate #3 of normal (no thermal injury) skin control

value: reduction mammoplasty; reduction mammoplasty; reduction mammoplasty; reduction mammoplasty; thigh lift

value: 0% (all samples)

value: F; F; F; F; F


title: Normal human (no thermal injury) skin pool control-2

source_name: Normal human skin, pooled replicate #2 of normal (no thermal injury) skin control

value: reduction mammoplasty; reduction mammoplasty; blepharoplasty; reduction mammoplasty; excision of redundant tissue (back)


title: Control tumor12

description: Control group


title: Control tumor8

description: Control group


title: Aurora-A tumor3

description: Experimental group


title: Aurora-A tumor8

description: Experimental group


title: Control tumor3

description: Control group


title: Control tumor7

description: Control group


title: Control tumor1

description: Control group


title: Aurora-A tumor2

description: Experimental group


title: Control tumor10

description: Control group


title: Aurora-A tumor6

description: Experimental group


title: Aurora-A tumor4

description: Experimental group


title: Aurora-A tumor1

description: Experimental group


title: Control tumor9

description: Control group


title: Control tumor5

description: Control group


title: Control tumor6

description: Control group


title: Control tumor11

description: Control group


title: Control tumor2

description: Control group


title: Control tumor4

description: Control group


title: Aurora-A tumor9

description: Experimental group


title: Burn wound margin pool >7 days post-thermal injury-3

source_name: Burn wound margin of human skin, replicate #3 of pooled time group >7 days post-thermal injury

value: excision, right lower extremity; excision, left foot; excision, abdomen; excision, right foot; excision, left upper extremity

value: M; M; M; M; M


title: Normal human (no thermal injury) skin pool control-1

source_name: Normal human skin, pooled replicate #1 of normal (no thermal injury) skin control

value: blepharoplasty; blepharoplasty; reduction mammoplasty; split-thickness skin grafting; blepharoplasty

value: F; M; F; M; F


title: Burn wound margin pool >7 days post-thermal injury-2

source_name: Burn wound margin of human skin, replicate #2 of pooled time group >7 days post-thermal injury

value: excision, right upper extremity; excision, chest; excision, right lower extremity; excision, right foot; excision, right hand

value: M; M; F; M; M


title: Burn wound margin pool 4-7 days post-thermal injury-1

source_name: Burn wound margin of human skin, replicate #1 of pooled time group 4-7 days post-thermal injury

value: excision, right upper extremity; excision, right upper extremity; excision, right flank; excision, chest; excision, chest

value: M; M; M; F; F


title: Burn wound margin pool 4-7 days post-thermal injury-3

source_name: Burn wound margin of human skin, replicate #3 of pooled time group 4-7 days post-thermal injury

value: excision, abdomen; excision, right upper extremity; excision, abdomen; excision, back; excision, right upper extremity


title: Burn wound margin pool 0-3 days post-thermal injury-3

source_name: Burn wound margin of human skin, replicate #3 of pooled time group 0-3 days post-thermal injury

value: excision, left hand; excision, back; excision, right upper extremity; excision, back; excision, right thigh


title: Burn wound margin pool 4-7 days post-thermal injury-2

source_name: Burn wound margin of human skin, replicate #2 of pooled time group 4-7 days post-thermal injury

value: excision, trunk; excision, left upper extremity; excision, right lower extremity; excision, trunk; excision, back

value: M; M; F; F; M


title: Female_Vir D12

status: Public on May 21 2010

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

description: This sample is Female Virgin Desiccation treatment, replicate 1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila mojavensis

source_name: Drosophila mojavensis (15081-1352.22)

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Flies were reared in opuntia/banana food in bottle at low density.  Adult flies were aged for 7 days in opuntia/banana vials (transferring once on day 4) prior to any treatmet.

extract_protocol: Total RNA extraction was performed using Invitrogen’s PureLink Micro-to-Midi Total Purification System.  The suggested manufacturer’s instructions were followed, which included a DNase I digestion to remove any possible genomic DNA contamination.  The quality and concentration of the RNA was determined using a NanoDrop spectrophotometer (NanoDrop Technologies).

treatment_protocol: The virgin treatment consisted of keeping the flies in male only or female only vials for eight days transferring them into fresh food vials once at day four.  The mated treatment was identical to the virgin treatment for the first seven days, at the beginning of the eighth day male and female vials were combined.  Flies remained in these mixed-sex vials for only 24 hours at which time they were separated by sex.  At the end of the eight-day period half of the flies from the virgin and mated treatments were placed in new food vials and half in a desiccator. The desiccator was composed of a 30 cm × 30 cm × 30 cm clear acrylic box.  Ambient air was pumped through two columns filled with 500 cm3 of Drierite desiccant into the chamber at a rate of 1.5 L per minute.  Additionally we placed inside the chamber a container filled with 200 cm3 of Drierite desiccant.  Empty 8-dram vials with either six males or females were capped using a cotton ball and placed inside the desiccator.  Relative humidity inside the chamber was sampled every minute using a HOBO relative humidity data logger (ONSET Computer Corporation).  The relative humidity throughout the experiment was maintained at less than 2%.  Prior to commencing the experiment the air in the chamber (with vials) was flushed for 15 minutes.  All flies were left inside the desiccator for 40 hours, at which point about 30% of the flies have died (LT30).  After this drying period, dead flies were aspirated and discarded while live flies were placed in groups of 15 in 1.5 mL tubes, snap frozen in liquid nitrogen and placed in a -80°C freezer until processing.

tag: sex

value: Female

tag: treatment

value: Virgin

value: Desiccation


title: Burn wound margin pool 0-3 days post-thermal injury-1

source_name: Burn wound margin of human skin, replicate #1 of pooled time group 0-3 days post-thermal injury

value: excision, abdomen; excision, right arm; excision, bilateral lower extremities; excision, back; excision, left hand

value: F; F; M; M; M


title: Burn wound margin pool 0-3 days post-thermal injury-2

source_name: Burn wound margin of human skin, replicate #2 of pooled time group 0-3 days post-thermal injury

value: excision, abdomen; excision, left lower extremity; excision, abdomen; excision, right foot; excision, left upper extremity

value: F; M; M; F; M


title: H1437 vector control

city: Los Angeles

first: Jane

last: Yanagawa

state: CA

department: Medicine

institute: UCLA

description: Gene expression data from H1437 lung cancer cell line stably transduced with an empty vector.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Gene Chip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed with an Affymetrix GeneChip Scanner 3000 7G. GCOS v1.4 was used for image processing.

data_processing: Harvard dChip software was used for data analysis.

source_name: Parental cell lines were purchased from the American Type Culture Collection.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: Cells were grown in 10% FBS/RPMI 1640 with L-glutamine containing 1% penicillin-streptomycin and 350µg/mL hygromycin B. Cells were maintained at confluencies between 50-80%.

extract_protocol: RNA was collected with the Qiagen RNeasy mini kit per kit instructions.

treatment_protocol: Cells were stably transduced as follows: wild-type Snail cDNA pcDNA3 (a gift from Dr. E. Fearon, University of Michigan) was excised from the plasmid with HindIII and EcoRV and subcloned into the retroviral vector pLHCX (Clontech, Mountain View, CA), which includes a drug resistance (hygromycin B) marker. All constructs were verified by restriction endonuclease digestion.  For virus production, 70% confluent 293T cells were co-transfected with pLHCX-Snail or pLHCX (vector alone).  Tumor cells were then transduced with high-titer supernatants producing either Snail or pLHCX virus.  Following transduction, the tumor cells were selected with hygromycin B. Cells were verified by genotyping and tested for mycoplasma prior to use in experiments. Cells were collected at similar confluencies for RNA extraction.

tag: histology

value: adenocarcinoma

tag: cell line


title: H441 Snail over-expressing

description: Gene expression data from H441 lung cancer cell line stably transduced with a Snail over-expressing vector.


title: GAF071003_THP1_LPS4

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: THP-1 Cells

label_protocol: standard Affymetrix procedures

extract_protocol:
PRINCIPLE: Cells are lysed and homogenized with guanidine isothiocyanate. RNA, in the presence of ETOH, binds to the silica based membrane.Contaminants are washed away and the RNA is eluted with DEPC water.
Method: THP-1 cells (2 x 106) were washed with cold HBSS. RLT buffer containing beta-Mercaptoethanol and guanidine isothiocyanate was added and cells were shredded in Qiashredder (Qiagen). Equal volume of 70% EtOH was added and passed through RNeasy mini spin column. Samples were treated with Dnase-1. RNA was finally washed and eluted in RNase free water. 2 ug RNA was used for microarray.

tag: cell type

value: THP-1 Cells

value: LPS (1 ug/ml) and Air


title: GAF071002_THP1_LPS1


title: Male_Vir D56

description: This sample is Male Virgin Desiccation treatment, replicate 2

value: Male


title: Male_Vir D12

description: This sample is Male Virgin Desiccation treatment, replicate 1


title: Male_Mat F12

description: This sample is Male Mated  Food treatment, replicate 1

value: Mated

value: Food


title: Female_Mat D34

description: This sample is Female Mated Desiccation treatment, replicate 2


title: GAF071003_THP1_LPS+CO4

value: LPS (1 ug/ml) and Carbon Monoxide (250 ppm)


title: Male_Vir F12

description: This sample is Male Virgin Food treatment, replicate 1


title: Male_Mat D54

description: This sample is Male Mated Desiccation treatment, replicate 2


title: Female_Mat D12

description: This sample is Female Mated  Desiccation treatment, replicate 1


title: Male_Mat D12

description: This sample is Male Mated  Desiccation treatment, replicate 1


title: GAF071003_THP1_CO5

value: Carbon Monoxide Gas (250 ppm)


title: GAF071002_THP1_LPS+CO1


title: Female_Mat F34

description: This sample is Female Mated Food treatment, replicate 2


title: Female_Vir F34

description: This sample is Female Virgin Food treatment, replicate 2


title: Female_Mat F12

description: This sample is Female Mated  Food treatment, replicate 1


title: GAF071003_THP1_CO4


title: GAF071002_THP1_CO1


title: Female_Vir F12

description: This sample is Female Virgin Food treatment, replicate 1


title: GAF071003_THP1_C4

value: Air


title: GAF071002_THP1_C1


title: GAF071003_THP1_LPS5


title: H441 vector control

description: Gene expression data from H441 lung cancer cell line stably transduced with an empty vector.


title: GAF071002_THP1_C2


title: H292 Snail over-expressing

description: Gene expression data from H292 lung cancer cell line stably transduced with a Snail over-expressing vector.

value: mucoepidermoid


title: H292 vector control

description: Gene expression data from H292 lung cancer cell line stably transduced with an empty vector.


title: GAF071002_THP1_LPS2


title: GAF071002_THP1_LPS3


title: H1437 Snail over-expressing

description: Gene expression data from H1437 lung cancer cell line stably transduced with a Snail over-expressing vector.


title: GAF071002_THP1_LPS+CO2


title: GAF071003_THP1_LPS+CO5


title: Male_Vir F34

description: This sample is Male Virgin Food treatment, replicate 2


title: Female_Vir D34

description: This sample is Female Virgin Desiccation treatment, replicate 2

value: Female


title: Male_Mat F54

description: This sample is Male Mated Food treatment, replicate 2


title: GAF071002_THP1_LPS+CO3


title: GAF071003_THP1_C5


title: GAF071002_THP1_CO2


title: GAF071002_THP1_CO3


title: GAF071002_THP1_C3


title: MTB strain 1254 Ctrl vs 10.0 mM H202 40min rep 2

status: Public on May 18 2010

first: Martin

middle: I

last: Voskuil

department: Microbiology

institute: University of Colorado Denver

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74740.gif

hyb_protocol: not provided

scan_protocol: GenePix GenePix

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mycobacterium tuberculosis

source_name: Strain: MTB strain 1254 Treatment: Control

label_protocol: TB-Synthesis and Labeling of cDNA SKlab 01; 1. Bring 0.5-5 ?g RNA (Typically 3 ?g) to 11 ?l and add 2 ?l (~2 mg/ml) random hexamers. 2. Heat 10 min at 65C (or 2 min at 98C), snap cool on ice. 10 rxns 20 rxns 3. Add 11?l 5.0 ?l 5X First-Strand buffer (51) (102) 2.5 ?l 100 mM DTT (25.5) (51) 2.0 ?l dNTP (5 mM A,G,C and 0.2 mM T) (20.5) (41) 1.5 ?l Cy3 or Cy5 (Typically use Cy5 for sample that should change) (15.3) (30.6) Then add 1.2-1.8 ?l Stratascript or 0.8-1.2 ?l Superscript II RTase. 4. Incubate 10m at 25C followed by 90m at 42C in PCR machine. Can freeze or leave at 4C o/n.; Protocol Type = Labeling; Performer: Martin,,Voskuil

extract_protocol: not provided

value: MTB strain 1254

value: Control

source_name: Strain: MTB strain 1254 Treatment: 10.0 mM H2O2 for 40 min

label_protocol:
TB-Slide Preparation SKlab 01; 1. Prepare NaOH-ethanol solution ?  dissolve NaOH in ddH2O 70 g / 280 mL 175 g / 700mL 200 g / 800 mL ?  stir until completely dissolved ?  add 95% ethanol 420 mL 1050 mL 1200mL ?  stir until completely mixed ?  if solution remains cloudy, add water until clear 2. Place slides in metal slide racks (30 slides/rack). Do not use defective slides. 3. Soak slides in the NaOH:EtOH:ddH2O solution for 2 hours with gentle rotation. 4. Rinse extensively with dH2O: ?  rinse each unit (slide/rack/container) vigorously with dH2O for 5 min ?  place slide racks in a large clean glass container, and tilt the container slightly for constant water flow. ?  wash under running water for 30 minutes. ?  do not allow the slides to dry at any time. It is critical to remove all traces of NaOH:EtOH. 5. Prepare poly-L-lysine solution in plastic container. ?  100 mL tissue culture PBS 800 mL Milli-Q water 100 mL poly-L-Lysine ?  We bring up the volume to about 1050 mL with Milli-Q water in order to submerge 3 racks of slides. ?  Mix well and split into 3 plastic containers. 6. Soak the slides in lysine solution for 45 min with shaking. Be sure to use a plastic container, because poly-L-lysine adheres to glass. Poly-L-Lysine solution may be reused. Keep the other slide filled racks in dH2O, while the first 3 are being coated. 7. After the lysine coating, rinse the slides by gently plunging up and down in 2 different changes of water. Spin dry 5' at 600 rpm. Place paper towels below rack to absorb liquid. 8. Store slides in a dessicator for 3 weeks prior to use. Slides that are older than 3 months may result in faint printing and higher background. Be sure to clean racks and containers thoroughly after each use. Built-up poly-L-Lysine on the sides of the containers may cause problems.; Protocol Type = Treatment; Performer: Martin,,Voskuil
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 1.5ug of total RNA; Parameter Type of label = Cy5; Performer: Martin,,Voskuil

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 250 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80; Performer: Martin,,Voskuil

extract_protocol:
not provided
TB-RNA Isolation and Purification SKlab 01; 1. Centrifuge 20-30 ml of early- to mid-log culture (O.D. 0.1-0.2) 4 min at 3700 rpm, at RT-37C. Pipette off supernatant and immediately freeze on dry ice and store at ?80C. 2. Add 1 ml Trizol (Gibco-BRL) to each of 4-8 pellets, suspend first pellet by vortexing,while other pellets are still frozen. Add suspension to 0.4 ml glass beads in a 2 ml screw cap tube. 3. Shake 30s at maximum speed in bead beater. Suspend next pellet and add to glass beads. Apply next sample to bead beater. Repeat bead beating two more times with each sample.Continue to periodically invert samples for at least 5 min in Trizol. 4. Centrifuge samples 45s at max speed, remove Trizol solution to a 2 ml screw cap tube containing half of the Heavy Phase Lock Gel I, supplied by 5 Prime 3 Prime, Inc. in 1.5 ml tubes and transferred with sterile stick to 2 ml tubes, and 300 ?l Chloroform:isoamyl alcohol (24:1). Invert rapidly for 15s, and continue inverting periodically for 2 min.a 5. Centrifuge 5-10m, remove aqueous layer (540 ?l) and add to a 1.5 ml tube containing 270 ?l isopropanol then add 270 ?l high salt solution (0.8M Na Citrate, 1.2M NaCl). Invert several times and spray with Staphene and remove from the P3. Typically ppted at 4C O/N. 6. Centrifuge 10m at 4C and remove isopropanol. Add 1 ml 75% EtOHb, invert several times and centrifuge 5m. 7. Remove EtOH by aspiration. Then, dry under vacuum for 2 min [Do not over dry]. 8. Suspend RNA in 90 ml RNase free water (don?t suspend in DNaseI buffer), may need to heat 10m at 55-60C to dissolve RNA. (Optional: obtain RNA concentration) 9. Add 10 ?l 10X DNaseI buffer to RNA (use no more than 80 ?g RNA) and add 4 ?l DNaseI (Ambion). Incubate 30m at 37C. Qiagen RNeasy purification. 1. Add 350 ?l RLT buffer (add 10 ?l BME to 1 ml RLT before using) and vortex. Add 260 ?l 95% EtOH (or 250 ?l 100% EtOH) to each sample and vortex. 2. Add to RNeasy spin column, centrifuge 15s, transfer column to a new 2 ml collection tube. Add 500 ?l RPE, centrifuge 15s, discard flow-through, add 500 ?l additional RPE and centrifuge 2m. If column still wet on sides, remove wash solution from tube and spin 1m to dry. 3. Transfer to a 1.5 ml collection tube, elute with 40 ?l RNase free water, centrifuge 1m. 4. Determine RNA concentration with A260/A280 readings. Dilute 1 ?l in 199 ?l TE. [200(dilution factor)x 40 ?g/A260x A260 = ?g/ml]. 5. Run 1 ?l RNA on 2% Agarose TAE gel. Run gel 45m at 100 volts. aIf Phase Lock Gel is not used, decrease Chloroform:isoamyl alcohol to 200?l. The yield will be less. Be careful not to remove any of the interface layer. bUsing 100% EtOH should be avoided in all steps of preparation of RNA intended for array analysis. Instead use 95% EtOH in preparation of solutions. Benzene contamination may fluoresce. cInstead of using the RNeasy purification, the DNaseI can be inactivated at 65-70C for 15m and then EtOH precipitated. The RNeasy purification may not be necessary in all applications. We find the purification gives more consistent results and is less time consuming, compared to precipitation. In addition, other purifications can be used. Note: The RNeasy column will remove much of the small tRNA and degraded RNA.; Protocol Type = Extract preparation; Performer: Martin,,Voskuil

value: 10.0 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 5.0 mM H202 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74732.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM H2O2 for 40 min

value: 5.0 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 0.5 mM H202 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74727.gif

source_name: Strain: MTB strain 1254 Treatment: 0.5 mM H2O2 for 40 min

value: 0.5 mM H2O2 for 40 min


title: Rhodospirillum rubrum triclosan 25 ug/l vs. reference

status: Public on May 19 2010

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Chronic exposure of Rhodospirillum rubrum to Triclosan (25ug l-1) in sistrom medium A.

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices©, USA). Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria.

data_processing: Microarray spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to built-in quality criteria. Quality check was performed for each array using the ArrayQuality package from BioConductor. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fit to a linear model and moderated t-statistics were calculated using empirical Bayes method. P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Rhodospirillum rubrum

source_name: Rhodospirillum rubrum unexposed to triclosan

label_protocol: Ten micrograms of RNA were reverse transcribed using Pronto kit (Promega, United States) following manufacturer’s instructions. Two color labeling, green for solvent control samples and red for condition (Triclosan challenge) samples, was performed using respectively Cy3-dCTP and Cy5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: Rhodospirillum rubrum S1H (54) was obtained from the American Type Culture Collection (ATCC 25903) and grown in Sistrom Medium A (SIS) with 0.2% (w/v) succinate as sole carbon source in dark aerobic conditions at 30°C and 50 rpm. Early stationary phase cells were inoculated at 2% (v/v) inoculum in 50 mL Sistrom medium. Prior to inoculation, SIS was spiked with equal final volumes of methanol to nullify the potential effect of differential solvent concentrations.

extract_protocol: Ten mL of cell suspension was harvested at OD680 = 0.4 from all test cultures with and without TCS and 20 mL RNAProtect Bacteria Reagent (QIAGEN) was added to preserve the RNA. The fixed cell suspensions were centrifuged at 3500 rpm for 10 min, the supernatant was removed, and pellets were stored at -80°C. The RNA extraction was performed using the RNeasy Midi Kit (QIAGEN), following the manufacturer’s guidelines. RNA quantity and quality was assessed using the Nanodrop ND-1000 and the 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Chip Kit following the manufacturer’s instructions. Only RNA with a RNA Integrity Number (RIN-) value of 9.5 and higher was used for microarray analysis.

treatment_protocol: Solvent control (Methanol)

tag: growth phase

value: mid-exponential

source_name: Rhodospirillum rubrum exposed to triclosan 25ug l-1

growth_protocol: Rhodospirillum rubrum S1H (54) was obtained from the American Type Culture Collection (ATCC 25903) and grown in Sistrom Medium A (SIS) with 0.2% (w/v) succinate as sole carbon source in dark aerobic conditions at 30°C and 50 rpm. Early stationary phase cells were inoculated at 2% (v/v) inoculum in 50 mL Sistrom medium. Prior to inoculation, SIS was spiked from a Triclosan (97.0% HPLC-grade, Fluka) stock solution in methanol and supplemented with equal final volumes of methanol to nullify the potential effect of differential solvent concentrations.

treatment_protocol: Rhodospirillum rubrum S1H was exposed to 25 ug l-1 Triclosan which was added prior to inoculation from a methanol stock. Total RNA was extracted when cultures reached mid-exponential phase (OD 680nm = 0.4).


title: MTB strain 1254 Ctrl vs 0.05 mM H202 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74721.gif

source_name: Strain: MTB strain 1254 Treatment: 0.05 mM H2O2 for 40 min

value: 0.05 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 10.0 mM H202 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74741.gif


title: MTB strain 1254 Ctrl vs 0.5 mM H202 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74726.gif


title: At_without DEX_T0

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

country: South Korea

institute: Kyung Hee University

description: Gene expression data from Arabidopsis leaf without DEX treatment for 0 hr.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The transgenic Arabidopsis (inducible expression of MYB46) plants were grown on soil in a growth chamber (16 h light/ 8 h dark) at 23 °C, after stratification.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: DEX (dexamethasone, Sigma) treatment was performed to the transgenic Arabidopsis (inducible expression of MYB46) plants were grown on soil for 14 days. DEX was dissolved in water to 1 mM stock and applied with spray at 10 µM with 0.02% silwet surfactant. In relevant experiments, control plants were treated with the same concentration of surfactant in water. After treatment, young rosette leaves (5th ~7th leaf) without petiole were harvested at the indicated times and frozen immediately with liquid N2, then stored until used.

value: Young rosette leaves (5-7th)

tag: genotype

value: Columbia (Col-0)

tag: age

value: 14-days old soil grown seedling


title: MTB strain1254 vs MTB strain 1254 for H2O2 exp control rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74756.gif

source_name: Strain: MTB strain 1254 Tretment: No Treatment

value: No Treatment


title: MTB strain 1254 Ctrl vs 50.0 mM H202 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74747.gif

source_name: Strain: MTB strain 1254 Treatment: 50.0 mM H2O2 for 40 min

value: 50.0 mM H2O2 for 40 min


title: At_with DEX_T1

description: Gene expression data from Arabidopsis leaf with DEX treatment for 1 hr.


title: At_with DEX_T6

description: Gene expression data from Arabidopsis leaf with DEX treatment for 6 hr.


title: Rhodospirillum rubrum triclosan 10 ug/l vs. reference

description: Chronic exposure of Rhodospirillum rubrum to Triclosan (10ug l-1) in sistrom medium A.

source_name: Rhodospirillum rubrum exposed to triclosan 10ug l-1

extract_protocol: Ten mL of cell suspension was harvested at OD680 = 0.4 from all test cultures with and without TCS and 20 mL RNAProtect Bacteria Reagent (QIAGEN) was added to preserve the RNA. The fixed cell suspensions were centrifuged at 3500 rpm for 10 min, the supernatant was removed, and pellets were stored at -80°C. The RNA extraction was performed using the RNeasy Midi Kit (QIAGEN), following the manufacturer’s guidelines. RNA quantity and quality was assessed using the Nanodrop ND-1000 and the 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Chip Kit following the manufacturer’s instructions. Only RNA with a RNA Integrity Number (RIN-) value of 9.5 and higher was used for microarray analysis

treatment_protocol: Rhodospirillum rubrum S1H was exposed to 10 ug l-1 Triclosan which was added prior to inoculation from a methanol stock. Total RNA was extracted when cultures reached mid-exponential phase (OD 680nm = 0.4).


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 4hrs rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83724.gif

source_name: Strain: MTB strain 1254 Treatment: 0.5 mM DETA/NO for 4hrs

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 4 hrs; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 261 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil

value: 0.5 mM DETA/NO for 4hrs


title: MTB strain 1254 Ctrl vs 0.05 mM H202 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83716.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 253 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19037.gif

scan_protocol: GenePix

label_protocol: TB-Synthesis and Labeling of cDNA SKlab 01; 1. Bring 0.5-5 ?g RNA (Typically 3 ?g) to 11 ?l and add 2 ?l (~2 mg/ml) random hexamers. 2. Heat 10 min at 65C (or 2 min at 98C), snap cool on ice. 10 rxns 20 rxns 3. Add 11?l 5.0 ?l 5X First-Strand buffer (51) (102) 2.5 ?l 100 mM DTT (25.5) (51) 2.0 ?l dNTP (5 mM A,G,C and 0.2 mM T) (20.5) (41) 1.5 ?l Cy3 or Cy5 (Typically use Cy5 for sample that should change) (15.3) (30.6) Then add 1.2-1.8 ?l Stratascript or 0.8-1.2 ?l Superscript II RTase. 4. Incubate 10m at 25C followed by 90m at 42C in PCR machine. Can freeze or leave at 4C o/n.; Protocol Type = Labeling; Performer: Kevin,,Visconti

source_name: Strain: MTB strain 1254 Treatment: 1.0 mM DETA/NO for 40min

label_protocol:
TB-Slide Preparation SKlab 01; 1. Prepare NaOH-ethanol solution ?  dissolve NaOH in ddH2O 70 g / 280 mL 175 g / 700mL 200 g / 800 mL ?  stir until completely dissolved ?  add 95% ethanol 420 mL 1050 mL 1200mL ?  stir until completely mixed ?  if solution remains cloudy, add water until clear 2. Place slides in metal slide racks (30 slides/rack). Do not use defective slides. 3. Soak slides in the NaOH:EtOH:ddH2O solution for 2 hours with gentle rotation. 4. Rinse extensively with dH2O: ?  rinse each unit (slide/rack/container) vigorously with dH2O for 5 min ?  place slide racks in a large clean glass container, and tilt the container slightly for constant water flow. ?  wash under running water for 30 minutes. ?  do not allow the slides to dry at any time. It is critical to remove all traces of NaOH:EtOH. 5. Prepare poly-L-lysine solution in plastic container. ?  100 mL tissue culture PBS 800 mL Milli-Q water 100 mL poly-L-Lysine ?  We bring up the volume to about 1050 mL with Milli-Q water in order to submerge 3 racks of slides. ?  Mix well and split into 3 plastic containers. 6. Soak the slides in lysine solution for 45 min with shaking. Be sure to use a plastic container, because poly-L-lysine adheres to glass. Poly-L-Lysine solution may be reused. Keep the other slide filled racks in dH2O, while the first 3 are being coated. 7. After the lysine coating, rinse the slides by gently plunging up and down in 2 different changes of water. Spin dry 5' at 600 rpm. Place paper towels below rack to absorb liquid. 8. Store slides in a dessicator for 3 weeks prior to use. Slides that are older than 3 months may result in faint printing and higher background. Be sure to clean racks and containers thoroughly after each use. Built-up poly-L-Lysine on the sides of the containers may cause problems.; Protocol Type = Treatment; Performer: Kevin,,Visconti
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 1.5ug of total RNA; Parameter Type of label = Cy5; Performer: Kevin,,Visconti

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 250 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80; Performer: Kevin,,Visconti

extract_protocol:
not provided
TB-RNA Isolation and Purification SKlab 01; 1. Centrifuge 20-30 ml of early- to mid-log culture (O.D. 0.1-0.2) 4 min at 3700 rpm, at RT-37C. Pipette off supernatant and immediately freeze on dry ice and store at ?80C. 2. Add 1 ml Trizol (Gibco-BRL) to each of 4-8 pellets, suspend first pellet by vortexing,while other pellets are still frozen. Add suspension to 0.4 ml glass beads in a 2 ml screw cap tube. 3. Shake 30s at maximum speed in bead beater. Suspend next pellet and add to glass beads. Apply next sample to bead beater. Repeat bead beating two more times with each sample.Continue to periodically invert samples for at least 5 min in Trizol. 4. Centrifuge samples 45s at max speed, remove Trizol solution to a 2 ml screw cap tube containing half of the Heavy Phase Lock Gel I, supplied by 5 Prime 3 Prime, Inc. in 1.5 ml tubes and transferred with sterile stick to 2 ml tubes, and 300 ?l Chloroform:isoamyl alcohol (24:1). Invert rapidly for 15s, and continue inverting periodically for 2 min.a 5. Centrifuge 5-10m, remove aqueous layer (540 ?l) and add to a 1.5 ml tube containing 270 ?l isopropanol then add 270 ?l high salt solution (0.8M Na Citrate, 1.2M NaCl). Invert several times and spray with Staphene and remove from the P3. Typically ppted at 4C O/N. 6. Centrifuge 10m at 4C and remove isopropanol. Add 1 ml 75% EtOHb, invert several times and centrifuge 5m. 7. Remove EtOH by aspiration. Then, dry under vacuum for 2 min [Do not over dry]. 8. Suspend RNA in 90 ml RNase free water (don?t suspend in DNaseI buffer), may need to heat 10m at 55-60C to dissolve RNA. (Optional: obtain RNA concentration) 9. Add 10 ?l 10X DNaseI buffer to RNA (use no more than 80 ?g RNA) and add 4 ?l DNaseI (Ambion). Incubate 30m at 37C. Qiagen RNeasy purification. 1. Add 350 ?l RLT buffer (add 10 ?l BME to 1 ml RLT before using) and vortex. Add 260 ?l 95% EtOH (or 250 ?l 100% EtOH) to each sample and vortex. 2. Add to RNeasy spin column, centrifuge 15s, transfer column to a new 2 ml collection tube. Add 500 ?l RPE, centrifuge 15s, discard flow-through, add 500 ?l additional RPE and centrifuge 2m. If column still wet on sides, remove wash solution from tube and spin 1m to dry. 3. Transfer to a 1.5 ml collection tube, elute with 40 ?l RNase free water, centrifuge 1m. 4. Determine RNA concentration with A260/A280 readings. Dilute 1 ?l in 199 ?l TE. [200(dilution factor)x 40 ?g/A260x A260 = ?g/ml]. 5. Run 1 ?l RNA on 2% Agarose TAE gel. Run gel 45m at 100 volts. aIf Phase Lock Gel is not used, decrease Chloroform:isoamyl alcohol to 200?l. The yield will be less. Be careful not to remove any of the interface layer. bUsing 100% EtOH should be avoided in all steps of preparation of RNA intended for array analysis. Instead use 95% EtOH in preparation of solutions. Benzene contamination may fluoresce. cInstead of using the RNeasy purification, the DNaseI can be inactivated at 65-70C for 15m and then EtOH precipitated. The RNeasy purification may not be necessary in all applications. We find the purification gives more consistent results and is less time consuming, compared to precipitation. In addition, other purifications can be used. Note: The RNeasy column will remove much of the small tRNA and degraded RNA.; Protocol Type = Extract preparation; Performer: Kevin,,Visconti

value: 1.0 mM DETA/NO for 40min


title: MTB strain 1254 Ctrl vs 5.0 mM H202 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74733.gif


title: MTB strain 1254 Ctrl vs 10.0 mM H202 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74739.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 4 hrs; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 250 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18438.gif

source_name: Strain: MTB strain 1254 Treatment: 0.05 mM DETA/NO for 40min

value: 0.05 mM DETA/NO for 40min


title: At_with DEX_T3

description: Gene expression data from Arabidopsis leaf with DEX treatment for 3 hr.


title: At_without DEX_T3

description: Gene expression data from Arabidopsis leaf without DEX treatment for 3 hr.


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19036.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 4hrs rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83725.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 4 hrs; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 262 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: At_without DEX_T1

description: Gene expression data from Arabidopsis leaf without DEX treatment for 1 hr.


title: At_without DEX_T6

description: Gene expression data from Arabidopsis leaf without DEX treatment for 6 hr.


title: MTB strain 1254 Ctrl vs 200 mM H202 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74749.gif

source_name: Strain: MTB strain 1254 Treatment: 200 mM H2O2 for 40 min

value: 200 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 0.05 mM H202 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74722.gif


title: MTB strain1254 vs MTB strain 1254 for H2O2 exp control rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74754.gif


title: MTB strain1254 vs MTB strain 1254 for H2O2 exp control rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74755.gif


title: MTB strain 1254 Ctrl vs 200 mM H202 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74752.gif


title: MTB strain1254 vs MTB strain 1254 for H2O2 exp control rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83714.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 251 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 5.0 mM H202 4hr rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74737.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM H2O2 for 4hrs

value: 5.0 mM H2O2 for 4hrs


title: MTB strain 1254 Ctrl vs 0.5 mM H202 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83717.gif

value: MTB strain 1254

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 254 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain1254 vs MTB strain 1254 for H2O2 exp control rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83713.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 250 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 50.0 mM H202 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74745.gif

value: Control


title: MTB strain 1254 Ctrl vs 200 mM H202 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74753.gif


title: MTB strain 1254 Ctrl vs 200 mM H202 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83723.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 260 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 5.0 mM H202 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74731.gif


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74762.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM DETA/NO for 40min

value: 5.0 mM DETA/NO for 40min


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18443.gif


title: MTB strain 1254 Ctrl vs 0.05 mM H202 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74723.gif


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19038.gif


title: MTB strain1254 vs MTB strain 1254 for DETA/NO exp control rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74766.gif


title: MTB strain 1254 Ctrl vs 50.0 mM H202 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74746.gif


title: MTB strain1254 vs MTB strain 1254 for H2O2 exp control rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83715.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 252 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 0.5 mM H202 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74728.gif


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74758.gif


title: MTB strain 1254 Ctrl vs 5.0 mM H202 4hr rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74738.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19041.gif

source_name: Strain: MTB strain 1254 Treatment: 0.5 mM DETA/NO for 40min

value: 0.5 mM DETA/NO for 40min


title: MTB strain1254 vs MTB strain 1254 for DETA/NO exp control rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74763.gif


title: MTB strain 1254 Ctrl vs 0.05 mM H202 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74724.gif

source_name: Strain: MTB strain 1254 Treatment: Control


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19044.gif


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19046.gif


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18442.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74770.gif


title: MTB strain 1254 Ctrl vs 50.0 mM H202 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83721.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 258 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19033.gif

source_name: Strain: MTB strain 1254 Treatment: 0.005 mM DETA/NO for 40min

value: 0.005 mM DETA/NO for 40min


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19045.gif


title: MTB strain 1254 Ctrl vs 0.5 mM H202 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74729.gif

value: 0.5 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19032.gif


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19034.gif


title: MTB strain 1254 Ctrl vs 10.0 mM H202 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74743.gif

source_name: Strain: MTB strain 1254 Treatment: 10.0 mM H2O2 for 40 min

value: 10.0 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74759.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74769.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19042.gif


title: MTB strain 1254 Ctrl vs 200 mM H202 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74751.gif


title: MTB strain 1254 Ctrl vs 0.5 mM H202 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74730.gif

source_name: Strain: MTB strain 1254 Treatment: 0.5 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74768.gif


title: MTB strain1254 vs MTB strain 1254 for DETA/NO exp control rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74764.gif


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18441.gif


title: MTB strain 1254 Ctrl vs 50.0 mM H202 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83722.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 259 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain1254 vs MTB strain 1254 for DETA/NO exp control rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74767.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 4hrs rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83727.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 4 hrs; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 264 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 5.0 mM H202 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74734.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM H2O2 for 40 min

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 250 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80; Performer: Martin,,Voskuil

value: 5.0 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 50.0 mM H202 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74748.gif


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74761.gif


title: MTB strain 1254 Ctrl vs 5.0 mM H202 4hr rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74736.gif


title: MTB strain 1254 Ctrl vs 5.0 mM H202 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83719.gif

label_protocol: TB-Slide Preparation SKlab 01; 1. Prepare NaOH-ethanol solution ?  dissolve NaOH in ddH2O 70 g / 280 mL 175 g / 700mL 200 g / 800 mL ?  stir until completely dissolved ?  add 95% ethanol 420 mL 1050 mL 1200mL ?  stir until completely mixed ?  if solution remains cloudy, add water until clear 2. Place slides in metal slide racks (30 slides/rack). Do not use defective slides. 3. Soak slides in the NaOH:EtOH:ddH2O solution for 2 hours with gentle rotation. 4. Rinse extensively with dH2O: ?  rinse each unit (slide/rack/container) vigorously with dH2O for 5 min ?  place slide racks in a large clean glass container, and tilt the container slightly for constant water flow. ?  wash under running water for 30 minutes. ?  do not allow the slides to dry at any time. It is critical to remove all traces of NaOH:EtOH. 5. Prepare poly-L-lysine solution in plastic container. ?  100 mL tissue culture PBS 800 mL Milli-Q water 100 mL poly-L-Lysine ?  We bring up the volume to about 1050 mL with Milli-Q water in order to submerge 3 racks of slides. ?  Mix well and split into 3 plastic containers. 6. Soak the slides in lysine solution for 45 min with shaking. Be sure to use a plastic container, because poly-L-lysine adheres to glass. Poly-L-Lysine solution may be reused. Keep the other slide filled racks in dH2O, while the first 3 are being coated. 7. After the lysine coating, rinse the slides by gently plunging up and down in 2 different changes of water. Spin dry 5' at 600 rpm. Place paper towels below rack to absorb liquid. 8. Store slides in a dessicator for 3 weeks prior to use. Slides that are older than 3 months may result in faint printing and higher background. Be sure to clean racks and containers thoroughly after each use. Built-up poly-L-Lysine on the sides of the containers may cause problems.; Protocol Type = Treatment; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 0.05 mM H202 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74725.gif

value: 0.05 mM H2O2 for 40 min


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74757.gif


title: MTB strain 1254 Ctrl vs 10.0 mM H202 40min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83720.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 257 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18440.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 4hrs rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83726.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 4 hrs; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 263 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18439.gif


title: MTB strain 1254 Ctrl vs 200 mM H202 40min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74750.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74760.gif


title: MTB strain1254 vs MTB strain 1254 for DETA/NO exp control rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74765.gif


title: MTB strain 1254 Ctrl vs 5.0 mM H202 40min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83718.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Starting OD = 0.15; Parameter Elapsed Time = 40 min; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Growth Vessel Volume = 255 ml; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80.; Performer: Martin,,Voskuil


title: HT-29_ctrl#3

status: Public on May 14 2010

city: Tokyo

first: Naomi

last: Haga

address: 3-10-6 Ariake, Koto-ku

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from human cancer cell lines. Control experiment.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)

tag: disease

value: colorectal adenocarcinoma

tag: mtdna

value: present

tag: stress

value: control

tag: inhibitor

tag: time


title: HT-29_GS#3

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_Pt_ContvsCont_select_Signal.CHP(HT-29_ctrl#3)

value: GS


title: MTB strain 1254 Ctrl vs 10.0 mM H202 40min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74742.gif

tag: strain


title: HT-1080_ctrl#2

value: fibrosarcoma


title: HT-1080_ctrl#3


title: HT-29(rho0)_ctrl#1

value: deficient


title: HT-1080(rho0)_ctrl#1


title: HT-1080_ctrl#5


title: HT-29_GS#2

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_Cont-2vsCont_select.CHP(HT-29_ctrl#2)


title: HT-1080_ctrl#1


title: HT-29_ctrl#1


title: HT-1080(rho0)_ctrl#2


title: HT-1080_TM+Rot

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)

value: TM

value: Rot


title: HT-1080_ctrl#6


title: HT-1080_TM


title: HT-29_GS#1

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_Cont.CHP(HT-29_ctrl#1)


title: HT-1080_GS#1

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont.CHP(HT-1080_ctrl#1)


title: HT-1080_2DG#1

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-2vsCont_select.CHP(HT-1080_ctrl#2)


title: HT-1080_2DG#3

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont_vsCont_select.CHP(HT-1080_ctrl#5)


title: HT-1080_ctrl#4


title: HT-1080(rho0)_TM

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_rho0_Cont-2vsrho0_Cont_select.CHP(HT-1080(rho0)_ctrl#2)


title: HT-29_ctrl#2


title: HT-29(rho0)_GS

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_rho0_Cont.CHP(HT-29(rho0)_ctrl#1)


title: HT-1080_GS#2


title: HT-1080_2DG#2

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-4vsCont_select.CHP(HT-1080_ctrl#4)


title: HT-1080_TM+AA

value: AA


title: HT-1080_GS+Rot_S

tag: supernatant

value: yes


title: HT-1080_GS+Rot


title: HT-1080_GS+AA_S


title: HT-1080(rho0)_GS_S


title: HT-1080_GS+VST

value: VST


title: HT-29_GS+VST

source_name: HT-29_GS+VST, 18h


title: HT-1080(rho0)_2DG

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_rho0_Cont.CHP(HT-1080(rho0)_ctrl#1)


title: HT-1080_2DG+Bu

description: Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-3vsCont_select.CHP(HT-1080_ctrl#3)

value: Bu


title: HT-1080_2DG+AA


title: HT-1080_2DG+Met

value: Met


title: HT-1080_2DG+Rot


title: HT-1080_2DG+Phen

value: Phen


title: HMFC 184Fb7p.2 Prestasis

status: Public on May 12 2010

city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

description: Human Cell Lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HT_HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Raw probe level intensities were processed for background correction, normalization and summarization using Probel level linear (PLM) model in LIMMA module(v.2.16.3) of Bioconductor package.

label: Biotin

source_name: HMFC

label_protocol: For each sample, the RNA target is prepared by annealing 2.0µg of total RNA in 5µl water with 5µl of 10µM T7 (Oligo dt) primer. First and second strand cDNA synthesis is performed and the cDNA products purified using magnetic beads. Labeled cRNA is synthesized from the cDNA using T7 RNA polymerase followed by clean-up with magnetic beads. Purified cRNA is quantitated and fragmented.

growth_protocol: Finite life span HMEC and HMFC from Specimens 184, 48 and 240L were obtained from reduction mammoplasty tissue of women  aged 21, 16, and 19 respectively. HMEC were grown starting from organoids in either serum free MCDB170 medium, or the serum-containing M85+CT±X medium described in this publication.  HMFC were grown in DME/F12+FCS+I

extract_protocol: Cell were lysed with trizol reagent (Invitrogen) according manufacturer's protocol. RNA was resuspended in 100 µl nuclease free water and subject to a second step purification on ion exchange column (Qiagen)

treatment_protocol: Cell cultures grown in the indicated media were harvested and different points in their growth from early passage good growing to near stasis, agonescence, or senescence.

value: mammary fibroblast cell

tag: individual

tag: passage

tag: growth status

value: Growing


title: HMFC 48Fb21p.2 Senescent

description: Human Cell Lines

value: Senescent


title: HMEC 250MK4pM85X.1 Prestasis

description: Human Cell Lines

source_name: HMEC

value: mammary epithelial cell

value: Growing-Prestasis


title: HMFC 184Fb15p.1 Senescent

description: Human Cell Lines


title: HMFC 184Fb7p.1 Prestasis

description: Human Cell Lines


title: HMFC 184Fb15p.2 Senescent

description: Human Cell Lines


title: HMFC 48Fb21p.1 Senescent

description: Human Cell Lines


title: HMFC 48Fb6p.3 Prestasis

description: Human Cell Lines


title: HMEC 250MK3pM85X.1 Prestasis

description: Human Cell Lines


title: HMFC 48Fb6p.2 Prestasis

description: Human Cell Lines


title: HMEC 240L5 Postselection

description: Human Cell Lines

value: Growing-Postselection


title: HMEC 240L10X Stasis

description: Human Cell Lines

value: Stasis


title: HMEC 48RT15X Stasis

description: Human Cell Lines


title: HMEC 240L6 Postselection

description: Human Cell Lines


title: HMEC 240L8X Intermediate

description: Human Cell Lines

value: Intermediate-Prestasis


title: HMEC 240L5X Prestasis

description: Human Cell Lines


title: HMEC 240L11X Stasis

description: Human Cell Lines


title: HMEC 240L2X Prestasis

description: Human Cell Lines


title: HMEC 48RT12X Intermediate

description: Human Cell Lines


title: HMEC 48RT16X Stasis

description: Human Cell Lines


title: HMEC 48RT3X Prestasis

description: Human Cell Lines


title: HMEC 48RT8X Intermediate

description: Human Cell Lines


title: HMEC 48RT10X Intermediate

description: Human Cell Lines


title: HMEC 48RT5X Prestasis

description: Human Cell Lines


title: HMEC 48RT4pM85 Prestasis

description: Human Cell Lines


title: HMEC 48RS22p170IP.1 Agonesence

description: Human Cell Lines

value: Agonesence-Postselection


title: HMEC 48RS11p170IP Postselection

description: Human Cell Lines


title: HMEC 48RT12pM85.1 Stasis

description: Human Cell Lines


title: HMEC 48RS11p170IP.2 Postselection

description: Human Cell Lines


title: HMEC 48RT12pM85.2 Stasis

description: Human Cell Lines


title: HMEC 184D14pM85X.2 Stasis

description: Human Cell Lines


title: HMEC 48RS11p170IP.1 Postselection

description: Human Cell Lines


title: HMEC 184B8p170IP Postselection

description: Human Cell Lines


title: HMEC 184D14pM85X.1 Stasis

description: Human Cell Lines


title: HMEC 48RT2pM85 Prestasis

description: Human Cell Lines


title: HMEC 184B9 PostSelection

description: Human Cell Lines

value: PostSelection


title: HMEC 184B14.1 Agonesence

description: Human Cell Lines


title: HMEC 184D9pM85.2 Stasis

description: Human Cell Lines


title: HMEC 184D2pM85X Prestasis

description: Human Cell Lines

value: Prestasis


title: HMEC 184B14.2 Agonesence

description: Human Cell Lines


title: HMEC 184D9pM85.1 Stasis

description: Human Cell Lines


title: HMEC 48RS22p170IP.2 Agonesence

description: Human Cell Lines


title: HMEC 184D11pM85X Intermediate

description: Human Cell Lines


title: HMEC 184D4p Prestasis

description: Human Cell Lines


title: SRA_8

city: Townsville

first: Jonathan

last: Golledge

state: Queensland

address: School of Medicine

department: School of Medicine

country: Australia

institute: James Cook University

hyb_protocol: 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Bioarrays (GE Healthcare) in hybridization buffer. Arrays were hybridized at 37ºC for 18 hrs in a temperature-controlled shaking incubator. Arrays were washed in 0.75x TNT at 46º C for 1 hr and stained with Cy5-Streptavidin dye conjugate for 30 min.

scan_protocol: Arrays were scanned with a GenePix™ 4000B scanner.

data_processing: Array data was processed with CodeLink Expression Analysis software (GE Healthcare) and data was analyzed with GeneSpring software (Silicon Genetics). To compare individual expression values across arrays, raw intensity data (generated from CodeLink Expression 2 software) from each gene was normalized to the median intensity of the array. Only genes which had values greater than the background intensity in at least one condition were used for further analysis.

label: biotin, Cy5-Streptavidin

source_name: Suprarenal region of abdominal aorta

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.35 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.

extract_protocol: RNA was extracted from excised artery segments by tissue disruption in Tri-Reagent (Sigma) and extraction as per manufacturers instructions. Isolated RNA was further purified on RNeasy columns (Qiagen) as per manufacturers instructions. The concentration and quality of total RNA was measured by spectrophotometry at OD260/280 and the quality of the total RNA sample was assessed using an Agilent Bioanalyser and Agilent RNA6000 Nano Lab Chip.

tag: ApoE-/- (C57B6 background), male mouse, 14 weeks old


title: HMEC 184D6X Intermediate

description: Human Cell Lines


title: HMEC 184D4pM85X Prestasis

description: Human Cell Lines


title: SRA_12


title: HMEC 184D6p.1 Intermediate

description: Human Cell Lines


title: IRA_6

source_name: Infrarenal region of abdominal aorta


title: SRA_1

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.54 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.


title: HMEC 184D2p Prestasis

description: Human Cell Lines


title: SRA_11

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.47 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.


title: SRA_6


title: IRA_11


title: IRA_8

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.34 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.


title: IRA_12

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.51 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.


title: Lee x Nova, at rind separation, 26 Oct 2006, rep 3

status: Public on May 08 2010

city: Riverside

first: Livia

last: Tommasini

address: 2150 Batchelor Hall

department: Botany and Plant Science

institute: University of California, Riverside

hyb_protocol: Ten µg labeled, fragmented cRNA was then hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip Hybridization Oven 320 on Affymetrix Barley1 Genechip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned on a Hewlett-Packard GeneArray scanner. cRNA preparation and hybridization were performed at University of California, Irvine Microarray Facility.

data_processing: GCOS MAS 5

organism: Citrus reticulata

source_name: Lee x Nova albedo tissue at the onset of rind separation

label_protocol: The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.

growth_protocol: Nules trees grown on Carrizo rootstock for 13 years at Lindcove Research and Extension Center, Exeter, CA.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) from frozen crown samples taken from above soil tissue excluding most fully extended lamina. The protocol is available on the Arabidopsis Information Resource website at http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/site2RnaL.htm. RNA was purified using Qiagen RNeasy spin columns with DNase treatment. Quality was assessed by running 25-250 ng on a RNA Lab-On-A-Chip (Caliper Technologies) using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Fruit from Nules, were harvested from 13-year-old field grown trees on Carrizo rootstock at Lindcove Research and Extension Center, Exeter, CA.,

tag: variety

value: Lee x Nova

tag: developmental stage

value: at rind separation

tag: tissue

value: albedo


title: foxo4 knock out mice without treatment

city: Dallas

first: wen

last: zhou

state: TX

address: 6000 Harry Hines Blvd NB11.110

department: Internal Medicine ,Cardiology

institute: UT Southwestern Medical Center at Dallas

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: colon mucosa

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: 8 weeks

tag: genetic modification

value: foxo4 knock out

value: Colon Mucosa

tag: treatment

value: untreated


title: foxo4 knock out mice two days after treatment of 250mg Trinitrobenzene Sulfonic Acid in 50% ethanol enema

description: replicate 3

tag: age


title: Lee x Nova, at rind separation, 26 Oct 2006, rep 2


title: wild type mice without treatment

description: replicate 6

value: wild type


title: foxo4 knock out mice  two days after treatment of 50% ethanol enema

description: replicate 4

value: 50% ethanol enema


title: Lee x Nova, after rind separation, 27 Nov 2006, rep 2

source_name: Lee x Nova albedo tissue after the onset of rind separation

value: after rind separation


title: Lee x Nova, after rind separation, 27 Nov 2006, rep 3


title: Lee x Nova, at rind separation, 26 Oct 2006, rep 1


title: Lee x Nova, after rind separation, 27 Nov 2006, rep 1


title: wild type mice two days after treatment of 250mg Trinitrobenzene Sulfonic Acid in 50% ethanol enema

description: replicate 1


title: Lee x Nova, before rind separation, Sep 14, 2006, rep 1

source_name: Lee x Nova albedo tissue before rind separation

value: before rind separation


title: Lee x Nova, before rind separation, Sep 14, 2006, rep 3


title: Clementine Nules, at rind separation, 26 Oct 2006, rep 1

source_name: Clementine Nules albedo tissue at the onset of rind separation

value: Clementine Nules


title: IRA_1

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.44 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.


title: wild type mice two days after treatment of 50% ethanol enema

description: replicate 2


title: Lee x Nova, before rind separation, Sep 14, 2006, rep 2


title: Clementine Nules, before rind separation, Sep 14, 2006, rep 3

source_name: Clementine Nules albedo tissue before rind separation


title: HT-1080_2DG+VST

tag: disease

value: fibrosarcoma

tag: cell line

value: present

value: VST


title: R2 with array type wheat from Affymetrix

status: Public on May 04 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Resistance to herbicides in weeds can be due to alteration(s) in the gene encoding the herbicide target site, or to herbicide degradation via a deviation in plant general metabolism. If target-site-based resistance is easy to study, the multigenic control of metabolism-based resistance renders it much more complex to study. Metabolism-based resistance to herbicides represents the major part of herbicide resistance in black-grass. Its most likely basis is an overexpression of genes encoding enzymes degrading herbicides. We thus seek to identify such overexpressed genes by comparing the transcriptomes of resistant and sensitive black-grass individuals belonging to an F2 line segregating for two resistance genes. Given there are no genomic tools developed for black-grass, this approach will use heterologous hybridisation onto a wheat Affymetrix microarray.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Alopecurus myosuroides

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: tiller - 18-22 degres, 16h_8h (day&night) soil and sand

treatment_protocol: Name:Herbicide_Puma LS - environmental treatment - abiotic stress,fenoxaprop:quantity 1.2l/ha time 150min .

tag: type

value: mutant (vu05-006)

tag: harvest date

tag: genotype

value: resistant


title: Clementine Nules, after rind separation, 27 Nov 2006, rep 1

source_name: Clementine Nules albedo tissue after the onset of rind separation


title: Clementine Nules, at rind separation, 26 Oct 2006, rep 3


title: Clementine Nules, at rind separation, 26 Oct 2006, rep 2


title: Clementine Nules, before rind separation, Sep 14, 2006, rep 2


title: S1 with array type wheat from Affymetrix

growth_protocol: tiller - 18-22 degres and light: 16h soil and sand

value: sensitive


title: Clementine Nules, before rind separation, Sep 14, 2006, rep 1


title: petitr1 with array type wheat from Affymetrix

value: moderately resistant


title: R1 with array type wheat from Affymetrix


title: petitr2 with array type wheat from Affymetrix


title: S2 with array type wheat from Affymetrix


title: Trichophyton violaceum_genome_rep2

city: Beijing

first: Qi

last: Jin

state: Beijing

address: No.6 Rongjing East Street, BDA

country: China

institute: National Institute for Viral Disease Control and Prevention

description: no

hyb_protocol: The two-color labeled DNA were mixed and combined with 5μg human Cot1 and 2μg polyA, then dried to 10μl final volume. The 10μl two-labeled target DNA preparations were combined with 1.5μl 50×Denhardts,2.25ul 20×SSC,1.125μl yeast tRNA (25μg/μl),0.375μl 1M HEPES（pH 7.0）and 0.375μl 10% SDS. This hybridization mixture was incubated for 2 min at 100℃,and the total volume was applied to the microarray slides. The sildes were sealed in hybridization chambers and left overnight at 65℃.Followed hybridization, the slides were washed for 5min in 2×SSC,0.1%(w/v)SDS twice,5min 1×SSC twice, and 5min in 0.2×SSC twice before being spun dry and scanned with Axon GenePix 4100A scanner(Axon Instruments).

scan_protocol: The slides was scanned with Axon GenePix 4100A scanner(Axon Instruments). The raw data were produced and normlized by GenePix Pro 5.0 software.

data_processing: Signal intensities were background corrected then the background intensity was subtracted locally. To be included in further normlization analysis, spots had to have (1) a signal intensity 55% of which was greater than 2* the standard deviation of the median background signal, and (2) a SNR532 (signal-noise ratio) of>= 3. The normlization method was Ratio Of Medians of all Features equal to 1.

organism: Trichophyton violaceum

source_name: Trichophyton violaceum BMU02087

label_protocol: Genomic DNA were isolated from  YEPD cultures by using Plant DNA Extract Kit (Qiagen). 4ug genomic DNA were labeled by DNA Labeling Kit (Invitrogen). Test strains and labeled by Cy5-dCTP. Modification included 3μl Cy5-dCTP (Amersham) were used for each 50 μl labeling reaction. DNA were purified with the Qiaquick PCR Purification Kit (Qiagen).

growth_protocol: Trichophyton violaceum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

extract_protocol: Genomic DNA was prepared using the Plant DNA Extraction kit (Qiagen) according to manufacturer instructions.

tag: Trichophyton violaceum BMU02087 Genomic DNA

organism: Trichophyton rubrum

source_name: Trichophyton rubrum BMU01672

label_protocol: Genomic DNA were isolated from YEPD cultures by using Plant DNA Extract Kit (Qiagen). 4ug genomic DNA were labeled by DNA Labeling Kit (Invitrogen). T. rubrum BMU01672 was the reference strain and was labeled by Cy3-dCTP. Modification included 3μl Cy3-dCTP (Amersham) were used for each 50 μl labeling reaction.

growth_protocol: Trichophyton rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton rubrum BMU01672 Genomic DNA


title: Trichophyton ajelloi_genome_rep2

description: no

organism: Arthroderma uncinatum

source_name: Trichophyton ajelloi ATCC-28454

growth_protocol: Trichophyton ajelloi were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton ajelloi ATCC-28454 Genomic DNA

growth_protocol: Trichophyton rubrum  were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton rubrum BMU01672 genomic DNA


title: Trichophyton violaceum_genome_rep1

description: no

treatment_protocol: Trichophyton violaceum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

treatment_protocol: Trichophyton rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton mentagrophytes_genome_rep2

description: no

organism: Trichophyton benhamiae

source_name: Trichophyton mentagrophytes BMU03104

growth_protocol: Trichophyton mentagrophytes were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton mentagrophytes BMU03104 Genomic DNA


title: Trichophyton mentagrophytes_genome_rep1

description: no

treatment_protocol: Trichophyton mentagrophytes were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton soudanense_genome_rep3

description: no

organism: Trichophyton soudanense

source_name: Trichophyton soudanense ATCC-24583

growth_protocol: Trichophyton soudanense were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton soudanense ATCC-24583 Genomic DNA


title: Trichophyton violaceum_genome_rep3

description: no


title: Microsporum canis_genome_rep1

description: no

organism: Microsporum canis

source_name: Microsporum canis BMU02865

growth_protocol: Microsporum canis were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum canis BMU02865 Genomic DNA


title: Trichophyton ajelloi_genome_rep1

description: no

treatment_protocol: Trichophyton ajelloi were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

growth_protocol: Trichophyton  rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Microsporum nanum_genome_rep2

description: no

organism: Nannizzia nana

source_name: Microsporum nanum ATCC-42129

growth_protocol: Microsporum nanum  were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum nanum ATCC-42129 genomic DNA

treatment_protocol: Trichophyton rubrum  were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Microsporum gallinae_genome_rep1

description: no

organism: Lophophyton gallinae

source_name: Microsporum gallinae ATCC-12108

growth_protocol: Microsporum gallinae were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum gallinae ATCC-12108 Genomic DNA

treatment_protocol: Trichophyton  rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton verrucosum_genome_rep3

description: no

organism: Trichophyton verrucosum

source_name: Trichophyton verrucosum BMU03357

growth_protocol: Trichophyton verrucosum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton verrucosum BMU03357 Genomic DNA


title: Microsporum gallinae_genome_rep2

description: no

treatment_protocol: Microsporum gallinae were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Microsporum canis BMU_genome_rep3

description: no

treatment_protocol: Microsporum canis were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton terrestre_genome_rep1

description: no

organism: Arthroderma terrestre

source_name: Trichophyton terrestre ATCC-28573

growth_protocol: Trichophyton terrestre were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton terrestre ATCC-28573 Genomic DNA


title: Trichophyton verrucosum_genome_rep2

description: no

treatment_protocol: Trichophyton verrucosum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton verrucosum_genome_rep1

description: no


title: Microsporum racemosum_genome_rep2

description: no

organism: Nannizzia racemosa

source_name: Microsporum racemosum ATCC-38556

growth_protocol: Microsporum racemosum  were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum racemosum ATCC-38556 Genomic DNA


title: Trichophyton ajelloi_genome_rep3

description: no


title: Microsporum racemosum_genome_rep1

description: no

growth_protocol: Microsporum racemosum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton schoenleinii_genome_rep3

description: no

organism: Trichophyton schoenleinii

source_name: Trichophyton schoenleinii ATCC-22775

growth_protocol: Trichophyton schoenleinii were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton schoenleinii ATCC-22775 Genomic DNA


title: Trichophyton mentagrophytes_genome_rep3

description: no


title: Trichophyton terrestre_genome_rep2

description: no

treatment_protocol: Trichophyton terrestre were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton schoenleinii_genome_rep2

description: no

treatment_protocol: Trichophyton schoenleinii were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton schoenleinii ATCC-22775 genomic DNA


title: Trichophyton terrestre_genome_rep3

description: no


title: Microsporum canis BMU_genome_rep2

description: no


title: Trichophyton  megninii_genome_rep3

description: no

source_name: Trichophyton megninii ATCC-2106

growth_protocol: Trichophyton  megninii were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton  megninii ATCC-2106 Genomic DNA


title: Trichophyton longifusum_genome_rep2

description: no

organism: Trichophyton longifusum

source_name: Trichophyton longifusum ATCC-22397

growth_protocol: Trichophyton longifusum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton longifusum ATCC-22397 Genomic DNA


title: Microsporum racemosum_genome_rep3

description: no

treatment_protocol: Microsporum racemosum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Microsporum gypseum_genome_rep1

description: no

organism: Nannizzia gypsea

source_name: Microsporum gypseum ATCC-24102

growth_protocol: Microsporum gypseum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum gypseum ATCC-24102 Genomic DNA


title: Trichophyton longifusum_genome_rep1

description: no

treatment_protocol: Trichophyton longifusum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Microsporum gypseum_genome_rep2

description: no

treatment_protocol: Microsporum gypseum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Microsporum nanum_genome_rep3

description: no

growth_protocol: Microsporum nanum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum nanum ATCC-42129 Genomic DNA

growth_protocol: Trichophyton rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton  soudanense_genome_rep2

description: no

data_processing: Signal intensities were background corrected then the background intensity was subtracted locally. To be included in further normlization analysis, spots had to have (1) a signal intensity 55% of which was greater than 2* the standard deviation of the median background signal, and (2) a SNR532 (signal-noise ratio) of>= 3. The normlization method was Ratio Of Medians of all Features equals to 1.

growth_protocol: Trichophyton  soudanense were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton  soudanense ATCC-24583 genomic DNA

tag: Trichophyton  rubrum BMU01672 genomic DNA


title: Microsporum gallinae_genome_rep3

description: no

tag: Trichophyton rubrum BMU01672 genomic DNA


title: Microsporum distortum_genome_rep1

description: no

organism: Microsporum distortum

source_name: Microsporum distortum ATCC-26224

growth_protocol: Microsporum distortum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum distortum ATCC-26224 Genomic DNA

tag: Trichophyton  rubrum BMU01672 Genomic DNA


title: Trichophyton  erinacei_genome_rep1

description: no

source_name: Trichophyton erinacei ATCC-28446

label_protocol: Genomic DNA were isolated from YEPD cultures by using Plant DNA Extract Kit (Qiagen). 4ug genomic DNA were labeled by DNA Labeling Kit (Invitrogen). Test strains and labeled by Cy5-dCTP. Modification included 3μl Cy5-dCTP (Amersham) were used for each 50 μl labeling reaction. DNA were purified with the Qiaquick PCR Purification Kit (Qiagen).

growth_protocol: Trichophyton erinacei were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton erinacei ATCC-28446 Genomic DNA


title: Microsporum distortum_genome_rep2

description: no

treatment_protocol: Microsporum distortum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton longifusum_genome_rep3

description: no


title: Microsporum gypseum_genome_rep3

description: no


title: Trichophyton  schoenleinii_genome_rep1

description: no

growth_protocol: Trichophyton  schoenleinii were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton  schoenleinii ATCC-22775 Genomic DNA


title: Microsporum cookei_genome_rep3

description: no

organism: Paraphyton cookei

source_name: Microsporum cookei ATCC-34662

growth_protocol: Microsporum cookei were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum cookei ATCC-34662 Genomic DNA


title: Microsporum cookei_genome_rep2

description: no

treatment_protocol: Microsporum cookei were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

source_name: Trichophyton rubrum BMU01672

growth_protocol: Trichophyton  rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton  erinacei_genome_rep2

description: no

growth_protocol: Trichophyton  erinacei  were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton  erinacei ATCC-28446 genomic DNA


title: Microsporum distortum_genome_rep3

description: no


title: Microsporum  canis ATCC_genome_rep3

description: no

source_name: Microsporum canis ATCC-36299

growth_protocol: Microsporum canis were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Microsporum  canis ATCC-36299 genomic DNA


title: Trichophyton  soudanense_genome_rep1

description: no

treatment_protocol: Trichophyton  soudanense were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.


title: Trichophyton  megninii_genome_rep2

description: no

growth_protocol: Trichophyton megninii were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton  megninii ATCC-2106


title: Microsporum  canis ATCC_genome_rep2

description: no

tag: Microsporum  canis ATCC-36299 Genomic DNA